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      The complete mitochondrial genome of a species of Cirrhipathes de Blainville, 1830 from Kauaʻi, Hawaiʻi (Hexacorallia: Antipatharia)

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          Abstract

          This study reports the first mitogenome from the antipatharian (black coral) genus Cirrhipathes (GenBank accession number ON653414). The 20,452 bp mitochondrial genome of Cirrhipathes cf . anguina LS-2022 consists of 13 protein-coding genes, two rRNA genes, and two tRNA genes ( trnM and trnW). The mitogenome is typical of other antipatharian families, including an A + T biased (64.1%) base composition and cytochrome c oxidase subunit I ( COX1) intron with embedded homing endonuclease gene ( HEG). A phylogenetic tree based on complete mitogenome sequences of currently available antipatharians indicates Cirrhipathes cf . anguina LS-2022 is sister and closely related to Stichopathes sp. SCBUCN-8849. However, it seems unlikely that intergeneric taxa share 99.97% similarity across their complete mitogenomes, raising questions about the current taxonomy of this group. This study highlights the need for additional vouchered antipatharian species to be sequenced so phylogenetic relationships can be compared with accepted taxonomy.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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              SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

              The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
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                Author and article information

                Journal
                Mitochondrial DNA B Resour
                Mitochondrial DNA B Resour
                Mitochondrial DNA. Part B, Resources
                Taylor & Francis
                2380-2359
                1 February 2024
                2024
                1 February 2024
                : 9
                : 2
                : 223-226
                Affiliations
                [a ]Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa , Kāne‘ohe, HI, USA
                [b ]US Fish and Wildlife Service, Pacific Fish and Wildlife Office , Honolulu, HI, USA
                [c ]Ocean Exploration Trust , Honolulu, HI, USA
                Author notes

                Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2024.2310130.

                CONTACT Leah E. K. Shizuru lshizuru@ 123456hawaii.edu Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa , Kāne‘ohe, HI, USA
                Author information
                https://orcid.org/0009-0000-8280-7198
                https://orcid.org/0000-0002-3430-3451
                https://orcid.org/0000-0002-0456-4343
                https://orcid.org/0000-0001-6748-1388
                https://orcid.org/0000-0001-6339-4340
                Article
                2310130
                10.1080/23802359.2024.2310130
                10836483
                38313464
                84ae55e6-0ec3-4379-975a-f81e8de6fdac
                © 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

                History
                Page count
                Figures: 3, Tables: 0, Pages: 4, Words: 2812
                Categories
                Data Note
                MitoGenome Report

                black coral,hawaii,mesophotic coral ecosystem,stichopathes,antipathes

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